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Tabulate AE Focused (Dichotomous) Summaries

Source: R/tbl_ae_focus.R
tbl_ae_focus.Rd

Summarize dichotomous AE data. For example, report the rate of patients that have an AE of Grade 3 or higher.

Usage

tbl_ae_focus(
  data,
  include,
  id,
  ae,
  soc = NULL,
  strata = NULL,
  label = NULL,
  id_df = NULL,
  statistic = "{n} ({p})",
  digits = NULL,
  sort = NULL,
  zero_symbol = "\U2014"
)

Arguments

data

Data frame

include

Vector of column names to summarize. Column names may be quoted or unquoted. All columns must be class 'logical'.

id

Variable name of the patient ID

ae

Variable name of the adverse event column

soc

Variable name of the system organ class column

strata

Variable to stratify results by, e.g. report AEs summaries by treatment group

label

A named list of labels that will be applied in the resulting table. Names must be those passed in include=. Default is NULL, and either the label attribute or the column name will be used.

id_df

Optional data frame of complete id values and strata to achieve correct base n for the situation in which not all subjects experience adverse events. See df_patient_characteristics for an example id_df that pairs with df_adverse_events.

statistic

String indicating the statistics that will be reported. The default is "{n} ({p})"

digits

Specifies the number of decimal places to round the summary statistics. By default integers are shown to zero decimal places, and percentages are formatted with style_percent(). If you would like to modify either of these, pass a vector of integers indicating the number of decimal places to round the statistics. For example, if the statistic being calculated is "{n} ({p}%)" and you want the percent rounded to 2 decimal places use digits = c(0, 2). User may also pass a styling function: digits = style_sigfig

sort

Controls order of AEs and SOCs in output table. The default is NULL, where AEs and SOCs are sorted alphanumerically (and factors sorted according to their factor level). Use sort = "ae" to sort AEs in decreasing frequency order, sort = "soc" to sort SOCs in decreasing order, and sort = c("ae", "soc") to sort both. AEs are sorted within SOC.

zero_symbol

String used to represent cells with zero counts. Default is the em-dash ("\U2014"). Using zero_symbol = NULL will print the zero count statistics, e.g. "0 (0)"

Value

a 'tbl_ae_focus' object

Example Output

Example 1

Examples

# \donttest{
# Example 1 -----------------------------------------------------------------
tbl_ae_focus_ex1 <-
  df_adverse_events %>%
  tbl_ae_focus(
    include = c(any_complication, grade3_complication),
    id = patient_id,
    ae = adverse_event,
    soc = system_organ_class,
    label =
      list(any_complication = "Any Grade Complication",
           grade3_complication = "Grade 3+ Complication")
  ) %>%
  bold_labels()
  # }